Re: AW: update: segmentation faults with AMBER topology and RAMD tcl scripts

From: Vlad Cojocaru (Vlad.Cojocaru_at_h-its.org)
Date: Thu Feb 25 2010 - 03:02:25 CST

Hi Francesco,

"Works fine" means RAMD works as well or only standard simulations work ?
Assuming RAMD works as well with your new compilation .................

The error with the if statements clearly comes from tcl8.3 ... I could
reproduce it here after I installed tcl8.3.5 and compiled namd against
it... It does not appear with tcl 8.4.19. I am also very confused. I do
not understand why these completely trivial if statements create
problems in tcl8.3. It looks as if it has something to do with the "eq"
operand ...

Unfortunately I am not able to compile NAMD with tcl8.5. The compilation
seem to work fine but then NAMD exits with segmentation faults and this
independent of tcl forces being on of off and independent of the NAMD
version ( I tried the CVS code from august last year and from
yesterday). I don't know what is wrong, but at the moment I cannot test
with tcl8.5 .

In a separate email, I'll send you the version I modified to be
compatible with tcl8.3. It would be nice if you could try it with your
old compilations of NAMD (the ones you used before and got the syntax
error )

Thanks for the help with testing ...

Vlad

Francesco Pietra wrote:
> Hello Vlad:
>
> Back from the roof, I have just checked that the CVS nightly build
> works fine like namd_2.7b2 with my system, CHARMM topologies, charmm
> ff. From what you write now, it seems that you assume that namd
> binaries, including nightly builds, are compiled for tcl< 8.4
>
> Debian lenny:
> tclsh
> % info tclversion
> 8.4
>
> > From the tk console of VMD 1.8.7, tcl version is 8.5
>
> I must say that I am now rather confused about all these versions, but
> if you want that I try the tcl8.3 version of ramd with my system with
> charmm topologies, please make it available, or send it to me. I'll
> try (although I don't expect it will turn useful).
>
> As to the error messages when using ramd with my (perfectly
> equilibrated) system, charmm topologies, with both builds of namd:
>
> ###############
> Fatal error on PE 0> FATAL ERROR: syntax error in expression "
> $mdSteps == 0&& $mdStart eq "yes" "
> ("if" test expression)
> while compiling
> "if { $mdSteps == 0&& $mdStart eq "yes" } {
> print "RAMD: WARNING: 'mdStart' has no meaning for pure RAMD simulation"
> }"
> (in namespace eval "::RAMD" script line 65)
> invoked from within
> "namespace eval ::RAMD {
> print RAMD:
> print RAMD: -------------------------------------------------------------------
> print RAMD: Random Accele..."
> (file "/home/francesco/ramd-4.0/scripts/ramd-4.0_script.tcl" line 42)
> ###############
>
> Compare the above with the error you reported to Giacomo:
>
> &&&&&&&&&&&&&&&&
> FATAL ERROR: syntax error in expression " $mdSteps == 0&& $mdStart eq "yes" " )
> about the following if statement at line 106 in the 'ramd-4.0_script.tcl':
>
> if { $mdSteps == 0&& $mdStart eq "yes" } {
> print "RAMD: WARNING: 'mdStart' has no meaning for pure RAMD simulation"
> }
> &&&&&&&&&&&&&&&
>
> I vaguely remember that, instinctively, I removed the
>
> if { $mdSteps == 0&& $mdStart eq "yes" } statement
>
> from your script, as it did not apply to my system. But I got errors
> from other "if" statements.
>
>
>
> Regards
> francesco
>
>
>
>
>
>
>
> On Wed, Feb 24, 2010 at 12:52 PM, Vlad Cojocaru<Vlad.Cojocaru_at_h-its.org> wrote:
>
>> Balazs,
>>
>> Great ! Thanks for the effort to compile .
>> To use the AMBER force field, it looks as if you need to compile older CVS
>> code (8 August 2009 works for sure) of namd2.7 or namd 2.6 .
>>
>> Francesco,
>>
>> So it seems that if the new CVS code is compiled against tcl8.4.19, the RAMD
>> scripts run with the CHARMM force field with no error message. Could you
>> confirm that as well ?
>> I also have a new version of the RAMD that is compatible with tcl8.3 ... It
>> seems that tcl8.3 does not like the "eq" operand and some if statements with
>> multiple tests ... Don't ask me why ...
>>
>> other NAMD users,
>>
>> Is there anybody that is able to run the new CVS code with AMBER topology
>> files ?
>>
>> Greetings
>> Vlad
>>
>> Balazs Jojart wrote:
>>
>>> Dear Vlad,
>>> The namd-CVS version was compiled against Tcl8.4.19.
>>> The RAMD calculations runs with charmm psf files, without any error
>>> message, but with this compilation I obtain again a segmentation fault error
>>> with the amber topology files.
>>> Don't worry about the troubles, we thank for your work to implement the
>>> code into namd.
>>> Cheers,
>>> Balazs
>>>
>>> Vlad Cojocaru wrote:
>>>
>>>> Dear Balazs,
>>>>
>>>> Did you try to run the tcl forces tutorials from the NAMD website? Do
>>>> they run correctly ? If you did not, I suggest you do that first. Like this
>>>> we will see if you have a general tcl problem or its only the RAMD scripts.
>>>> Let me know about it ... I am saying this because I had similar problems
>>>> with tcl 8.5 with other tcl scripts I have been using ( like the former ABF
>>>> module )...
>>>>
>>>> If the tcl forces tutorials exit with the same type of errors, then there
>>>> is a general problem with your compilation. If these errors only appear
>>>> while running RAMD, then the next test would be if you could compile against
>>>> tcl 8.4.19 ...
>>>>
>>>> Actually maybe to put a correct diagnostic, you could compile namd 2.6
>>>> both against tcl 8.4.19 and 8.5 and try the RAMD scripts with this NAMD code
>>>> ....
>>>>
>>>> What is actually interesting that you don't get the seg faults anymore
>>>> although you are using AMBER topology. ....
>>>>
>>>> I am also trying to test against different tcl versions to see what is
>>>> actually going wrong . ....
>>>>
>>>> Sorry for the troubles .... but we are running these scripts so
>>>> successfully here that I didn't even imagine that all these errors could
>>>> appear ...
>>>>
>>>> Vlad
>>>>
>>>> Balazs Jojart wrote:
>>>>
>>>>> Dear Vlad,
>>>>> I think the topology is OK, because it was used in a former simulation
>>>>> only using standard MD. In the output file (RAMD), the the structure
>>>>> information looks ok. I tested the loadcoords part as well, by adding "puts
>>>>> coordinates(1)" lines in the tcl code, and the coordinates are also missing
>>>>> - same error "no such element in array".
>>>>> Our system administrator compiled the newest CVS of namd against tcl8.5,
>>>>> fortunately I don't obtain any segfault error, but unfortunately, the same
>>>>> error was occurred with the example files as well, as described below. The
>>>>> outputs are attached.
>>>>> Do we have to compile with another version of tcl (for example
>>>>> Tcl8.4.19)?
>>>>> Cheers,
>>>>> Balazs
>>>>>
>>>>> Cojocaru,Vlad wrote:
>>>>>
>>>>>> Dear Balazs,
>>>>>>
>>>>>> This is a more friendly error ...
>>>>>> It looks as if your definition of the ramd and/or protein atoms is
>>>>>> somehow wrong .. You have an atom that somehow does not have a mass .. Can
>>>>>> you double check ?
>>>>>>
>>>>>> Otherwise, if you could send me a zipped file with the files required
>>>>>> to reproduce your problem (topology, coordinates, box info files) I can try
>>>>>> to see what is wrong ..
>>>>>>
>>>>>> vlad
>>>>>>
>>>>>>
>>>>>> -----Urspr√ľngliche Nachricht-----
>>>>>> Von: Balazs Jojart [mailto:jojartb_at_gmail.com]
>>>>>> Gesendet: Di 23.02.2010 17:05
>>>>>> An: Cojocaru,Vlad
>>>>>> Betreff: Re: namd-l: update: segmentation faults with AMBER topology
>>>>>> and RAMD tcl scripts
>>>>>>
>>>>>> Dear Vlad,
>>>>>> Using the RAMD method with the compiled namd2.7beta2 against Tcl8.5
>>>>>> and charmm topologies I obtain the following error message:
>>>>>>
>>>>>> TCL: can't read "masses(5962)": no such element in array
>>>>>> FATAL ERROR: can't read "masses(5962)": no such element in array
>>>>>> while executing
>>>>>> "expr $ligMass + $masses($ramdAtom)"
>>>>>> ("foreach" body line 2)
>>>>>>
>>>>>> the whole error message is attached.
>>>>>> I'm going to test the charmm topologies, with the namd2.6 + tcl8.5
>>>>>> version compilation.
>>>>>> Cheers,
>>>>>> Balazs
>>>>>>
>>>>>>
>>>>>> Vlad Cojocaru wrote:
>>>>>>
>>>>>>> Dear all,
>>>>>>>
>>>>>>> To test the errors I've been commenting on recently I compiled today's
>>>>>>> CVS code of NAMD (23 February 2010) using exactly the same protocol as for
>>>>>>> my last running compilation (13 August 2009). Tcl version is tcl8.4.19.
>>>>>>> Architecture: x86_64 + infniband + intel 11.0 compiler + mvapich1.4rc1. The
>>>>>>> compilation worked absolutely fine.
>>>>>>>
>>>>>>> Then I ran the RAMD tests which resulted in "Segmentation violation" .
>>>>>>> Then I tested the new executable for one of my standard MD simulation using
>>>>>>> AMBER topology. The same undefined error occurred.
>>>>>>>
>>>>>>> To conclude, the latest CVS code produces segmentation faults on AMBER
>>>>>>> topologies regardless whether RAMD is switched on or not. Therefore, this
>>>>>>> error apparently has nothing to do with the RAMD scripts. It looks as if the
>>>>>>> amber topology is read correctly but the program exists with segmentation
>>>>>>> violation immediately after reading the topology (below last lines of the
>>>>>>> output)
>>>>>>>
>>>>>>> I could not test against CHARMM topologies as I don't have one but
>>>>>>> another NAMD user mentioned recently that the code runs fine on CHARMM
>>>>>>> topologies while observing the same errors with AMBER topologies.
>>>>>>>
>>>>>>> To test the RAMD scripts until the problem with the AMBER topologies
>>>>>>> will be fixed, I suggest to compile namd 2.6 against tcl8.4.19 or above.
>>>>>>> If you still see errors, please let me know.
>>>>>>>
>>>>>>> Cheers
>>>>>>> Vlad
>>>>>>>
>>>>>>> -----------------output sample------------------------------
>>>>>>> Reading parm file (1r9o_1.top) ...
>>>>>>> PARM file in AMBER 7 format
>>>>>>> Warning: Encounter 10-12 H-bond term
>>>>>>> Warning: Found 18886 H-H bonds.
>>>>>>> Info: SUMMARY OF PARAMETERS:
>>>>>>> Info: 62 BONDS
>>>>>>> Info: 131 ANGLES
>>>>>>> Info: 49 DIHEDRAL
>>>>>>> Info: 0 IMPROPER
>>>>>>> Info: 0 CROSSTERM
>>>>>>> Info: 0 VDW
>>>>>>> Info: 210 VDW_PAIRS
>>>>>>> Info: TIME FOR READING PDB FILE: 0.158216
>>>>>>> Info:
>>>>>>> Info: Reading from binary file 1r9o_1_eq10_rst.500000.coor
>>>>>>> Info: ****************************
>>>>>>> Info: STRUCTURE SUMMARY:
>>>>>>> Info: 64265 ATOMS
>>>>>>> Info: 64360 BONDS
>>>>>>> Info: 13994 ANGLES
>>>>>>> Info: 29662 DIHEDRALS
>>>>>>> Info: 0 IMPROPERS
>>>>>>> Info: 0 CROSSTERMS
>>>>>>> Info: 98534 EXCLUSIONS
>>>>>>> Info: 60475 RIGID BONDS
>>>>>>> Info: 132320 DEGREES OF FREEDOM
>>>>>>> Info: 22676 HYDROGEN GROUPS
>>>>>>> Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
>>>>>>> Info: 22676 MIGRATION GROUPS
>>>>>>> Info: 4 ATOMS IN LARGEST MIGRATION GROUP
>>>>>>> Info: TOTAL MASS = 394234 amu
>>>>>>> Info: TOTAL CHARGE = -1.48128e-05 e
>>>>>>> Info: MASS DENSITY = 1.00973 g/cm^3
>>>>>>> Info: ATOM DENSITY = 0.0991208 atoms/A^3
>>>>>>> Info: *****************************
>>>>>>> Info:
>>>>>>> Info: Entering startup at 30.2467 s, 156.332 MB of memory in use
>>>>>>> Info: Startup phase 0 took 0.00019908 s, 156.332 MB of memory in use
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>>
>> --
>> ----------------------------------------------------------------------------
>> Dr. Vlad Cojocaru
>>
>> Heidelberg Institute for Theoretical Studies
>> HITS gGmbH
>> Molecular and Cellular Modelling Group
>> Schloss-Wolfsbrunnenweg 35
>> 69118 Heidelberg
>>
>> Tel: ++49-6221-533202
>> Fax: ++49-6221-533298
>>
>> e-mail:Vlad.Cojocaru[at]h-its.org
>>
>> http://projects.villa-bosch.de/mcm/people/cojocaru/
>>
>> ----------------------------------------------------------------------------
>> Amtgericht Mannheim / HRB 337446
>> Managing Directors: Dr. h.c. Klaus Tschira, Prof. Dr.-Ing. Andreas Reuter
>> http://www.h-its.org (http://eml-research.de)
>> ----------------------------------------------------------------------------
>>
>>
>>
>>
>

-- 
----------------------------------------------------------------------------
Dr. Vlad Cojocaru
Heidelberg Institute for Theoretical Studies
HITS gGmbH
Molecular and Cellular Modelling Group
Schloss-Wolfsbrunnenweg 35
69118 Heidelberg
Tel: ++49-6221-533202
Fax: ++49-6221-533298
e-mail:Vlad.Cojocaru[at]h-its.org
http://projects.villa-bosch.de/mcm/people/cojocaru/
----------------------------------------------------------------------------
Amtgericht Mannheim / HRB 337446
Managing Directors: Dr. h.c. Klaus Tschira, Prof. Dr.-Ing. Andreas Reuter
http://www.h-its.org (http://eml-research.de)
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